There are a couple options. The easiest is to create a separate theme for each site by duplicating the Agency theme, changing the name of the folder so that its site related, and then change the name of the theme at the top of the style.css file too.

Using a site oriented naming convention for your themes will help you manage things as your multisite install grows.

The other option is to use the Genesis Simple Hooks plugin to modify your PHP. It’s Multisite compatible. Then you can use a plugin like the WordPress.com Safe CSS plugin to customize your CSS. Just know that Automattic stopped developing that plugin when the Borglike Jetpack absorbed it’s functionality.

Personally I wouldn’t put Jetpack on a Multisite install that has more than a few sites on it. But that’s me.